[English] 日本語
Yorodumi
- PDB-6e5v: human mGlu8 receptor amino terminal domain in complex with (S)-3,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e5v
Titlehuman mGlu8 receptor amino terminal domain in complex with (S)-3,4-Dicarboxyphenylglycine (DCPG)
ComponentsMetabotropic glutamate receptor 8
KeywordsSIGNALING PROTEIN / mGluR8 ATD / GRM8 / DCPG
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / regulation of synaptic transmission, glutamatergic / visual perception / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / G alpha (i) signalling events / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 8 / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 ...GPCR, family 3, metabotropic glutamate receptor 8 / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-HVG / Metabotropic glutamate receptor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsChen, Q. / Ho, J.D. / Ashok, S. / Vargas, M.C. / Wang, J. / Atwell, S. / Bures, M. / Schkeryantz, J.M. / Monn, J.A. / Hao, J.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structural Basis for ( S)-3,4-Dicarboxyphenylglycine (DCPG) As a Potent and Subtype Selective Agonist of the mGlu8Receptor.
Authors: Chen, Q. / Ho, J.D. / Ashok, S. / Vargas, M.C. / Wang, J. / Atwell, S. / Bures, M. / Schkeryantz, J.M. / Monn, J.A. / Hao, J.
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metabotropic glutamate receptor 8
B: Metabotropic glutamate receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2156
Polymers117,6652
Non-polymers5494
Water64936
1
A: Metabotropic glutamate receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1073
Polymers58,8331
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metabotropic glutamate receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1073
Polymers58,8331
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.945, 106.780, 117.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Metabotropic glutamate receptor 8 / mGluR8


Mass: 58832.715 Da / Num. of mol.: 2 / Mutation: C246S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM8, GPRC1H, MGLUR8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00222
#2: Chemical ChemComp-HVG / 4-[(S)-amino(carboxy)methyl]benzene-1,2-dicarboxylic acid / (S)-3,4-Dicarboxyphenylglycine (DCPG)


Mass: 239.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO6 / Comment: agonist*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100mM Bis-Tris, pH 6.5, 27% PEG 3350, 200mM Sodium Acetate

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→19.91 Å / Num. obs: 21256 / % possible obs: 99.3 % / Redundancy: 6.2 % / Net I/σ(I): 9.5
Reflection shellResolution: 2.95→3.11 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.91 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BSZ

6bsz


Resolution: 2.95→19.82 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.89 / SU B: 26.279 / SU ML: 0.467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.52
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1128 5.1 %RANDOM
Rwork0.2551 ---
obs0.2576 21256 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.15 Å2 / Biso mean: 66.96 Å2 / Biso min: 28.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å2-0 Å2
2---4.07 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 2.95→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6682 0 36 36 6754
Biso mean--53.92 48.26 -
Num. residues----882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196864
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9519331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.45874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68724.155296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.987151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7851536
X-RAY DIFFRACTIONr_chiral_restr0.0660.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215256
LS refinement shellResolution: 2.952→3.027 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 79 -
Rwork0.369 1452 -
all-1531 -
obs--96.84 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more